In silico detection of inhibitor potential of Passiflora compounds against SARS-Cov-2(Covid-19) main protease by using molecular docking and dynamic analyses.

SARS-Cov-2(Covid-19) is a new strain of coronavirus and was firstly emerged in December 2019 in Wuhan, China. Now, there is no known specific treatment of Covid-19 available. COVID-19 main protease is a potential drug target and is firstly crystallised by Liu et al (2020). In the study, we investigated the drug potential of molecules that the components of an important medicinal plant Passiflora by using molecular docking, molecular dynamic and drug possibility properties of these molecules. Docking performances were done by Autodock. Chloroquine, hydroxychloroquine were used as standarts for comparison of tested ligands. The molecular docking results showed that the Luteolin, Lucenin, Olealonic acid, Isoorientin, Isochaphoside, Saponarin, Schaftoside etc. ligands was bound with COVID-19 main protease above -8,0 kcal/mol binding energy. Besides, ADME, drug-likeness features of compounds of Passiflora were investigated using the rules of Lipinski, Veber, and Ghose. According to the results obtained, it has been shown that compounds of Passiflora have the potential to be an effective drug in the COVID-19 pandemic. Further studies are needed to reveal the drug potential of these ligands. Our results will be a source for these studies.

Introduction

Passiflora (passion flowers) is the largest genus of the family Passifloraceae. The species of this genus are distributed tropical regions of the World [1]. Many species of this genus have been found that contain anti-depressant properties. The leaves and the roots are generally more potent and have been used to improve the actions of mind-altering drugs. Few species of Passiflora have been studied according to its medicinal utility [2].

However, these plants have a major source of pharmacologically active compounds, including cytolysins, potential bactericid and anticancer drugs. For example, Passiflora quadrangularis is known with antihelminthic action and also often used to treat bronchitis, asthma, and whooping cough [3].

The new coronavirus type SARS-Cov 2 (severe acute respiratory syndrome), that appeared in December 2019 in China and became a global pandemic. There is not any specific treatment available so far. The viral particles effect both humans and animals, and can cause some serious infections of especially respiratory system. Besides, some drugs including chloroquine, remdesivir and hydroxychloroquine have been observed to be effective against Covid-19 [4].

Recent studies have shown that the genomic model of SARS-CoV 2 is comparable to other coronaviruses. It is stated that these viruses generally collect a few polypeptides in their life cycle and develop proteolytic degradation to produce 20 additional proteins. Among these proteases, it is emphasized that main protease (Mpro) and papain-like protease (PLpro) proteases are of vital importance in virus replication. Important studies have been done with these proteases to discover specific inhibitors against COVID-19. Yu et.al reported the calculation of the potential binding of luteolin and other natural components versus Mpro. It was concluded that luteolin also binds effectively with other target proteins of SARS-CoV-2 such as PLpro, Spike protein and RdRp [ 5 ].

An important therapeutic target for corona viruses is known to be the main protease, as this enzyme plays a key role in polyprotein processing and is active in a dimeric form [ 6 ]. Amin et al, 2021, stated that the main protease is the part of the replication machinery of the corona virus and can be used as a therapeutic target against the corona virus [ 7 ]. Li and Kang 2020, emphasized that the main protease encoded by the viral genome could be an attractive drug target, as it plays an important role in dividing viral polyproteins into functional proteins [ 8 ] In another study, it was noted that the sequence of the main protease is closely related to other betacoronaviruses and aids drug discovery studies based on previous lead compounds [ 9 ]. Ghosh et al., 2021, identified important molecular properties that regulate Mpro inhibitory properties [ 10 ]. All these studies reveal that the main protease is a suitable target for identifying potential drug substances. We also used the main protease in our study. Molecular docking is known a promising and useful tool for drug desing. In the present study, we investigated drug potential of Passiflora components against COVID-19 main (PDB ID: 6LU7). We aimed to find the most stable complex by revealing the binding energies.

Molecular docking is known a promising and useful tool for drug desing. In the present study, we investigated drug potential of Passiflora components against COVID-19 main (PDB ID: 6LU7). We aimed to find the most stable complex by revealing the binding energies.

Materials and methods

Molecular docking analyses

Molecular docking calculations were performed in Autodock Vina software [ 11 ]. The water molecules and cofactors were removed from the protein to clearly see the protein-ligand interation [ 12 ]. COVID-19 main protease used as a protein and the structure of this protein was freely available from the RCSB Protein Data Bank as a 3D theoretical model (PDB ID: 6LU7). Twenty nine ligands were tested. Ligands that used in the study and their properties were given in Table 1 (https://pubchem.ncbi.nlm.nih.gov/).

Table 1

Ligands used in the study and their properties.

No	Ligands	PubChem ID code	Molecular weight(g.mol−1)	Structure(3D)
1	Oleanolic acid	10,494	456.7 g/mol	Image, table 1
2	Luteolin	5,280,445	286.24 g/mol	Image, table 1
3	Beta-Sitosterol	222,284
	414.7 g/mol			Image, table 1
4	Beta-amyrin	73,145	426.7 g/mol	Image, table 1
5	Stigmasterol	5,280,794	412.7 g/mol	Image, table 1
6	Apigenin	5,280,443	270.24 g/mol	Image, table 1
7	Chrysin	5,281,607	254.24 g/mol	Image, table 1
8	6-Hydroxyflavone	72,279	238.24 g/mol	Image, table 1
9	Edulan-I	521,066	192.3 g/mol	Image, table 1
10	Edulan-II	6,432,428	192.3 g/mol	Image, table 1
12	Chimaphilin	101,211	186.21 g/mol	Image, table 1
13	Lucenin-2	442,615	610.5 g/mol	Image, table 1
14	Saponarin	441,381	594.5 g/mol	Image, table 1
15	Isoschaftoside	3,084,995	564.5 g/mol	Image, table 1
16	Schaftoside	442,658	564.5 g/mol	Image, table 1
17	Rutin	5,280,805	610.5 g/mol	Image, table 1
19	Isoorientin	114,776	448.4 g/mol	Image, table 1
20	Orientin	5,281,675	448.4 g/mol	Image, table 1
21	Isovitexin	162,350	432.4 g/mol	Image, table 1
21	5,6-benzoflavone	2361	272.3 g/mol	Image, table 1
22	Kaempferol	5,280,863	286.24 g/mol	Image, table 1
23	Harmalol	3565	200.24 g/mol	Image, table 1
24	Harman	5,281,404	182.22 g/mol	Image, table 1
25	Harmol	68,094	198.22 g/mol	Image, table 1
26	Harmaline	3564	214.26 g/mol	Image, table 1
27	Harmine	5,280,953	212.25 g/mol	Image, table 1
28	Remdevisir	121,304,016	602.6 g/mol	Image, table 1
29	Dexamethasone	5743	392.5 g/mol	Image, table 1

The binding potential of chloroquine and hydroxychloroquine has been reviewed as a control ligands. 2D structure of the ligands were converted to energy minimized 3D-structure. All protein and ligands were validated before performing the in silico computations [ 13 ].

Molecular dynamic analyses

The simulation of the ligand-protein complex was performed using the playmolecule software [ [14], [15], [16], [17], [18] ] (playmolecule.com). MD simulation was performed for 20 ns to check the stability of the ligand-protein complexes [ Fig. 1 ].

Fig. 1

Solvation box of 6lu7(playmolecule.com).

We determined the performance of MM/PB(GB)SA to identify the correct binding poses for ligands, including from the Schrödinger suite and Amber package (http://cadd.zju.edu.cn/farppi) [ 19 ].

Drug likeness and ADMET prediction for the components of Passiflora

Currently, computer-based ADME analyses are gaining for drug discovery [ 20 ]. Pharmacokinetics and drug-likeness prediction of drug candidate molecule(s) was performed by online tool SwissADME (http://www.sib.swiss) (http://www.swissadme.ch/index.php) [ 21 , 22 ]. In addition, these toxicological predictions have applied to Lipinski, Ghose, and Veber rules and bioavailability scores [ 23 – 25 ].

Results and discussion

Plant compounds have been always attractive from scientists to research novel drug development. The experimental and clinical studies are being continued for drug development, although several antiviral drugs used against Covid-19.

Molecular docking results obtained from this study indicated a strong interactions between COVID-19 main protease and potential drug candidates. The binding strength was defined by use of scoring function based on the Lamarckian Generic Algorithm. The binding free energy may include electrostatic, hydrogen bonding, and van der Waals interactions [ 12 ]. The least binding energy refers to the most stable binding between protein and the ligand The binding energy results calculated by Vina were presented in Table 2 [ Fig. 6 ]. All of the docked structures were visualized in VMD [ 26 ].

Table 2

Target protein and drug candidate molecules (ligands) molecular docking results.

Ligands	Binding Energy (kcal/mol)	H bound
Oleanolic acid	-9.5 kcal/mol	1Asp-A289
Luteolin	-8.3 kcal/mol	3Gln-A110Thr-A111Asn-A151
Beta-Sitosterol	-8.0 kcal/mol	0
Beta-amylin	-8.0 kcal/mol	0
Stigmasterol	-7.6 kcal/mol	1Arg-A105
Apigenin	-7.6 kcal/mol	1Lys-A137
Chrysin	-7.3 kcal/mol	3Asn-A238Asp-A197Lys-A137
6-Hydroxyflavone	-7.1 kcal/mol	1Glu-A270
Edulan-I	-6.5 kcal/mol	1Gln-A110
Edulan-II	-5.8 kcal/mol	0
Chimaphilin	-6.1 kcal/mol	2Thr-A111Gln-A110
Lucenin-2	-10.7 kcal/mol	4Phe-A219Leu-A220Arg-A222Asn-A274
Saponarin	-10.6 kcal/mol	3Arg-A40(2)Phe-A181
Isoschaftoside	-10.5 kcal/mol	3Arg-A222Asn-274Phe-A219
Schaftoside	-10.2 kcal/mol	5Asp-A197Asn-A238Arg-A131(2)Lys-A137
Rutin	-9.7 kcal/mol	5Arg-A131Lys-A137(2)Asp-A289(2)
Isoorientin	-9.2 kcal/mol	3Pro-A52Tyr-A54Phe-A181
Orientin	-8.7 kcal/mol	3Thr-A199Lys-A137Leu-A287
Isovitexin	-8.7 kcal/mol	3Glu-A55Pro-A52Tyr-A54
5,6-benzoflavone	-8.4 kcal/mol	1Gln-A110
Kaempferol	-7.5 kcal/mol	4Leu-A287Arg-A131Asp-A197Asn-A238
Harmalol	-6.0 kcal/mol	1Thr-A199
Harman	-5.8 kcal/mol	0
Harmol	-5.7 kcal/mol	0
Harmaline	-5.5 kcal/mol	0
Harmine	-5.4 kcal/mol	1Leu-A220
Remdesivir (Control)	-9.4 kcal/mol	1Lys-A137
Dexamethasone (Control)	-8.0 kcal/mol	3Lys-A137Thr-A198Tyr-A239

Fig. 6

(a) Binding free energy graph of Lucenin-2. (b) Binding free energy graph of Oleanolic acid. (c) Binding free energy graph of Isoorientin. (d) Binding free energy graph of Isoschaftoside. (e) Binding free energy graph of schaftoside. (f) Binding free energy graph of Saponarin. (g) Binding free energy graph of Remdivisir.

The Remdesivir and Dexamethasone which is control drugs, also binds to Covid-19 protein with considerable affinity (−9.4 and -8.0 kcal/mol, respectively). In this case, all the ligands have comparable binding affinity (−5.4 to −10.7 kcal/mol) (Figs. 2 –4 ).

Fig. 2

The energy distribution of protein [27,28].

Fig. 4

Representation of Isoorientin molecule at the active site of 6LU7 in molecular docking.

Representation of Isoschaftoside molecule at the active site of 6LU7 in molecular docking.

RSMD, a crucial parameter to analyze the equilibration of MD trajectories, is estimated for backbone atoms of the protein and ligand-protein complexes. Measurements of the backbone RMSD for the two complexes provided insights into the conformational stability. The comparisons of the RMSD value of ligands-protein are shown in Fig. 5 .

Fig. 5

(a) Lucenin2 and 6LU7 Molecular dynamic results. (b) Isoorientin and 6LU7 Molecular dynamic results. (c) Isoshaphoside and 6LU7 Molecular dynamic results. (d) Oleolanic acid and 6LU7 Molecular dynamic results. (e) Saponarin and 6LU7 Molecular dynamic results. (f) Schaftoside and 6LU7 Molecular dynamic results. (g) Molecular dynamic results of Remdevisir and 6lu7.

The RMSF of the backbone atoms of each residue in the ligand-protein complex was analyzed to observe the flexibility of the enzyme backbone structure. The high RMSF value shows more flexibility whereas the low RMSF value shows limited movements. The RMSF graph for ligands-protein complex is shown in Fig. 5 (a–g). According to molecular dynamic results, root mean square deviation (RMSD), root mean square fluctuation (RMSF) of Cα atoms as a function of residue number as a function of simulation time was used for studying the stability of the modeled domains during MD simulations. RMSD values of Isoorientin and Saponarin seem to be stable between 21 to 25 nanosecond.

Since molecular docking scoring did not indicate an acceptable prediction for ligand binding affinities, the MM/PB(GB)SA analyses were utilized to predict their binding affinities. MM/PB(GB)SA was determined to identify the binding free energy for ligands, including from the Schrödinger suite and Amber package (http://cadd.zju.edu.cn/farppi) [ 19 ]. In Fig. 6(a–g) was shown MM/PB(GB)SA graph of ligands

Furthermore, human intestinal absorption, aqueous solubility levels, BBB penetration, skin penetretion levels, CYP inhibition (CYP1A2, CYP3A4, CYP2C19, CYP2C6, CYP2D6), P-gp subsrate of compounds of Passiflora were evaluated by prediction models in this study. (Supplementery file).

Drug-likeness can be characterized as a complex balance of different structural properties that determines whether a compound is a drug. These features, mainly lipophilicity, hydrogen bonding properties, molecule size, and pharmacophoric features and many others [ 29 ]. In addition, drug-likeness results of compounds were shown in Tables 3 and 4 .

Table 3

Drug-likeness results of compounds.

Ligand	Drug likeness			Bioavalibility Score
	Lipinski	Ghose	Veber
Oleanolic acid	Yes1 violation: MLOGP>4.15	No3 violations: WLOGP>5.6, MR>130, #atoms>70	Yes	0.56
Luteolin	Yes	Yes	Yes	0.55
Beta-Sitosterol	Yes1 violation: MLOGP>4.15	No3 violations: WLOGP>5.6, MR>130, #atoms>70	Yes	0.55
Beta-amyrin	Yes1 violation: MLOGP>4.15	No3 violations: WLOGP>5.6, MR>130, #atoms>70	Yes	0.55
Stigmasterol	Yes1 violation: MLOGP>4.15	No3 violations: WLOGP>5.6, MR>130, #atoms>70	Yes	0.55
Apigenin	Yes	Yes	Yes	0.55
Chrysin	Yes	Yes	Yes	0.55
6-Hydroxyflavone	Yes	Yes	Yes	0.55
Edulan-I	Yes	Yes	Yes	0.55
Edulan-II	Yes	Yes	Yes	0.55
Chimaphilin	Yes	Yes	Yes	0.55
Lucenin-2	No; 3 violations: MW>500, NorO>10, NHorOH>5	No; 4 violations: MW>480, WLOGP<-0.4, MR>130, #atoms>70	No; 1 violation: TPSA>140	0.17
Saponarin	No; 3 violations: MW>500, NorO>10, NHorOH>5	No; 4 violations: MW>480, WLOGP<-0.4, MR>130, #atoms>70	No; 1 violation: TPSA>140	0.17
Isoschaftoside	No; 3 violations: MW>500, NorO>10, NHorOH>5
	No; 3 violations: MW>480, WLOGP<-0.4, MR>130	No; 1 violation: TPSA>140	0.17
Schaftoside	No; 3 violations: MW>500, NorO>10, NHorOH>5	No; 3 violations: MW>480, WLOGP<-0.4, MR>130	No; 1 violation: TPSA>140	0.17
Rutin	No; 3 violations: MW>500, NorO>10, NHorOH>5	No; 4 violations: MW>480, WLOGP<-0.4, MR>130, #atoms>70	No; 1 violation: TPSA>140	0.17
Isoorientin	No; 2 violations: NorO>10, NHorOH>5	No; 1 violation: WLOGP<-0.4	No; 1 violation: TPSA>140	0.17
Orientin	No; 2 violations: NorO>10, NHorOH>5	No; 1 violation: WLOGP<-0.4	No; 1 violation: TPSA>140	0.17
Isovitexin	Yes; 1 violation: NHorOH>5	Yes	No; 1 violation: TPSA>140	0.55
5,6-benzoflavone -	Yes	Yes	Yes	0.55
Kaempferol	Yes	Yes	Yes	0.55
Harmalol	Yes	Yes	Yes	0.55
Harman	Yes	Yes	Yes	0.55
Harmol	Yes	Yes	Yes	0.55
Harmaline	Yes	Yes	Yes	0.55
Harmine	Yes	Yes	Yes	0.55

Table 4

ADME results of compounds.

Ligands	Pharmacokinetics
Oleanolic acid	GI absorption	Low
BBB permeant	No
P-gp substrate	No
CYP1A2 inhibitor	No
CYP2C19 inhibitor	No
CYP2C9 inhibitor	No
CYP2D6 inhibitor	No
CYP3A4 inhibitor	No
Log Kp (skin permeation)	-3.77 cm/s
Luteolin	GI absorption	High
BBB permeant	No
P-gp substrate	No
CYP1A2 inhibitor	Yes
CYP2C19 inhibitor	No
CYP2C9 inhibitor	No
CYP2D6 inhibitor	Yes
CYP3A4 inhibitor	Yes
Log Kp (skin permeation)	-6.25 cm/s
Beta-Sitosterol	GI absorption	Low
BBB permeant	No
P-gp substrate	No
CYP1A2 inhibitor	No
CYP2C19 inhibitor	No
CYP2C9 inhibitor	No
CYP2D6 inhibitor	No
CYP3A4 inhibitor	No
Log Kp (skin permeation)	-2.20 cm/s
Beta-amyrin	GI absorption	Low
BBB permeant	No
P-gp substrate	No
CYP1A2 inhibitor	No
CYP2C19 inhibitor	No
CYP2C9 inhibitor	No
CYP2D6 inhibitor	No
CYP3A4 inhibitor	No
Log Kp (skin permeation)	-2.41 cm/s
Stigmasterol	GI absorption	Low
BBB permeant	No
P-gp substrate	No
CYP1A2 inhibitor	No
CYP2C19 inhibitor	No
CYP2C9 inhibitor	Yes
CYP2D6 inhibitor	No
CYP3A4 inhibitor	No
Log Kp (skin permeation)	-2.74 cm/s
Apigenin	GI absorption	High
BBB permeant	No
P-gp substrate	No
CYP1A2 inhibitor	Yes
CYP2C19 inhibitor	No
CYP2C9 inhibitor	No
CYP2D6 inhibitor	Yes
CYP3A4 inhibitor	Yes
Log Kp (skin permeation)	-5.80 cm/s
Chrysin	GI absorption	High
BBB permeant	Yes
P-gp substrate	No
CYP1A2 inhibitor	Yes
CYP2C19 inhibitor	No
CYP2C9 inhibitor	No
CYP2D6 inhibitor	Yes
CYP3A4 inhibitor	Yes
Log Kp (skin permeation)	-5.35 cm/s
6-Hydroxyflavone	GI absorption	High
BBB permeant	Yes
P-gp substrate	No
CYP1A2 inhibitor	Yes
CYP2C19 inhibitor	Yes
CYP2C9 inhibitor	No
CYP2D6 inhibitor	Yes
CYP3A4 inhibitor	Yes
Log Kp (skin permeation)	-5.18 cm/s
Edulan-I	GI absorption	High
BBB permeant	Yes
P-gp substrate	No
CYP1A2 inhibitor	No
CYP2C19 inhibitor	No
CYP2C9 inhibitor	No
CYP2D6 inhibitor	No
CYP3A4 inhibitor	No
Log Kp (skin permeation)	-5.36 cm/s
Edulan-II	GI absorption	High
BBB permeant	Yes
P-gp substrate	No
CYP1A2 inhibitor	No
CYP2C19 inhibitor	No
CYP2C9 inhibitor	No
CYP2D6 inhibitor	No
CYP3A4 inhibitor	No
Log Kp (skin permeation)	-5.36 cm/s
Chimaphilin	GI absorption	High
BBB permeant	Yes
P-gp substrate	No
CYP1A2 inhibitor	Yes
CYP2C19 inhibitor	Yes
CYP2C9 inhibitor	No
CYP2D6 inhibitor	No
CYP3A4 inhibitor	No
Log Kp (skin permeation)	-5.62 cm/s
Lucenin-2	GI absorption	Low
BBB permeant	No
P-gp substrate	No
CYP1A2 inhibitor	No
CYP2C19 inhibitor	No
CYP2C9 inhibitor	No
CYP2D6 inhibitor	No
CYP3A4 inhibitor	No
Log Kp (skin permeation)	-11.88 cm/s
Saponarin	GI absorption	Low
BBB permeant	No
P-gp substrate	Yes
CYP1A2 inhibitor	No
CYP2C19 inhibitor	No
CYP2C9 inhibitor	No
CYP2D6 inhibitor	No
CYP3A4 inhibitor	No
Log Kp (skin permeation)	-11.06 cm/s
Isoschaftoside	GI absorption	Low
BBB permeant	No
P-gp substrate	Yes
CYP1A2 inhibitor	No
CYP2C19 inhibitor	No
CYP2C9 inhibitor	No
CYP2D6 inhibitor	No
CYP3A4 inhibitor	No
Log Kp (skin permeation)	-11.30 cm/s
Schaftoside	GI absorption	Low
BBB permeant	No
P-gp substrate	Yes
CYP1A2 inhibitor	No
CYP2C19 inhibitor	No
CYP2C9 inhibitor	No
CYP2D6 inhibitor	No
CYP3A4 inhibitor	No
Log Kp (skin permeation)	-11.30 cm/s
Rutin	GI absorption	Low
BBB permeant	No
P-gp substrate	Yes
CYP1A2 inhibitor	No
CYP2C19 inhibitor	No
CYP2C9 inhibitor	No
CYP2D6 inhibitor	No
CYP3A4 inhibitor	No
Log Kp (skin permeation)	-10.26 cm/s
Isoorientin	GI absorption	Low
BBB permeant	No
P-gp substrate	No
CYP1A2 inhibitor	No
CYP2C19 inhibitor	No
CYP2C9 inhibitor	No
CYP2D6 inhibitor	No
CYP3A4 inhibitor	No
Log Kp (skin permeation)	-9.14 cm/s
Orientin	GI absorption	Low
BBB permeant	No
P-gp substrate	No
CYP1A2 inhibitor	No
CYP2C19 inhibitor	No
CYP2C9 inhibitor	No
CYP2D6 inhibitor	No
CYP3A4 inhibitor	No
Log Kp (skin permeation)	-9.14 cm/s
Isovitexin	GI absorption	Low
BBB permeant	No
P-gp substrate	No
CYP1A2 inhibitor	No
CYP2C19 inhibitor	No
CYP2C9 inhibitor	No
CYP2D6 inhibitor	No
CYP3A4 inhibitor	No
Log Kp (skin permeation)	-8.79 cm/s
5,6-benzoflavone	GI absorption	High
BBB permeant	Yes
P-gp substrate	No
CYP1A2 inhibitor	Yes
CYP2C19 inhibitor	Yes
CYP2C9 inhibitor	No
CYP2D6 inhibitor	No
CYP3A4 inhibitor	No
Log Kp (skin permeation)	-4.82 cm/s
Kaempferol	GI absorption	High
BBB permeant	No
P-gp substrate	No
CYP1A2 inhibitor	Yes
CYP2C19 inhibitor	No
CYP2C9 inhibitor	No
CYP2D6 inhibitor	Yes
CYP3A4 inhibitor	Yes
Log Kp (skin permeation)	-6.70 cm/s
Harmalol	GI absorption	High
BBB permeant	Yes
P-gp substrate	Yes
CYP1A2 inhibitor	Yes
CYP2C19 inhibitor	No
CYP2C9 inhibitor	No
CYP2D6 inhibitor	No
CYP3A4 inhibitor	No
Log Kp (skin permeation)	-6.28 cm/s
Harman	GI absorption	High
BBB permeant	Yes
P-gp substrate	Yes
CYP1A2 inhibitor	Yes
CYP2C19 inhibitor	No
CYP2C9 inhibitor	No
CYP2D6 inhibitor	No
CYP3A4 inhibitor	Yes
Log Kp (skin permeation)	-5.08 cm/s
Harmol	GI absorption	High
BBB permeant	Yes
P-gp substrate	No
CYP1A2 inhibitor	Yes
CYP2C19 inhibitor	No
CYP2C9 inhibitor	No
CYP2D6 inhibitor	No
CYP3A4 inhibitor	Yes
Log Kp (skin permeation)	-6.98 cm/s
Harmaline	GI absorption	High
BBB permeant	Yes
P-gp substrate	Yes
CYP1A2 inhibitor	Yes
CYP2C19 inhibitor	No
CYP2C9 inhibitor	No
CYP2D6 inhibitor	Yes
CYP3A4 inhibitor	No
Log Kp (skin permeation)	-6.14 cm/s
Harmine	GI absorption	High
BBB permeant	Yes
P-gp substrate	No
CYP1A2 inhibitor	Yes
CYP2C19 inhibitor	No
CYP2C9 inhibitor	No
CYP2D6 inhibitor	Yes
CYP3A4 inhibitor	Yes
Log Kp (skin permeation)	-4.94 cm/s

According to Lipinski's rule (Pfizer's rule, Lipinski's rule of five, RO5), the active drug has no more than one violation of the following properties including molecular weight(MW) ≤500, LogP ≤5, hydrogen bond acceptors ≤10, hydrogen bond donors ≤5 [ 23 ] .According to Veber rules, the active drug has total hydrogen bonds ≤ 12, rotatable bonds ≤ 10, and Polar surface area PSA (Polar surface area) ≤ 140 tend to have oral bioavailability ≥ 20% [ 25 ]. According to Ghose rules, active drug has Log P(-0.4 ~5.6), MR(Molar refractivity (40 ~150), MW(160 ~480), number of atoms(20 ~70), polar surface area (PSA) < 140 [ 24 ].

Based on the drug-likeness analysis, Oleanolic acid, Luteolin, Beta-sitosterol, Beta-Amyrin, Sterigmasterol, Apigenin, Chrysin, 6-Hydroxyflavone, Edulan I and II, Chimaphilin, Isovixetin, 5,6,-benzoflavone, Kaempferol, Harmalol, Harman, Harmol, Harmaline, Harmine were found in accordance with the Lipinski's, Veber or Ghose' rule. However, Lipinski's rule of five may not apply to natural compounds. The only half of all FDA-approved small-molecule drugs are both used and compatible with the ‘rule-of-five’ [ 30 ]. Therefore, it has the potential to be used as a medicine in other molecules.

Today, drug development studies are based on irreversible inhibitors. Covalent inhibition is also a method used to obtain irreversible inhibition. Irreversible inhibitors interact with target proteins and the reaction tends to be complete rather than stable. Covalent inhibitors have some important advantages over non-covalent ones. Covalent inhibitors may act on target proteins by superficial binding cleavage leading to the development of new inhibitors with higher potency than non-covalent inhibitors. Covalent drugs generally have stronger binding affinity to the target due to the covalent bond between the ligand and the protein. Thus, they show stronger potential while maintaining the size of pharmacologically advantageous small molecules. Covalent interaction with the target protein is an important point in terms of prolonging the duration of effect biologically. However, these inhibitors are a disadvantage as they tend to be toxic if they show off-target binding. Therefore, the presence of such inhibitors should be considered in drug development [ 31 ].

Conclusion

Perforatum sp. used for many years as a medicinal plant for different treatments, has recently become popular with research for its different properties. This medicinal plant has become available since the beneficial effects it on human health. In our research based on this useful plant, the possibility of being used as a medicine in SARS-Cov-2 pandemic that our country and all countries of the world have been fighting for a long time has been investigated. Based on the results, it was concluded that Perforatum could be effective on SARS-Cov-2, but it is necessary to conduct laboratory tests in vitro and in vivo on animals and patients to approve their validity in inhibiting Covid-19.

Declaration of Competing Interest

The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.